Modelling the empirical data

We first load a few packages and functions.

# Packages
  library(tidyverse)
  library(tidybayes)
  library(rethinking)
  library(patchwork)

# Functions
  r.srm <- readRDS("./functions/r.srm.rds")
  fp <- readRDS("./functions/fp.rds")
  sn <- readRDS("./functions/sn.rds")
  hist.plot <- readRDS("./functions/hist.plot.rds")
  
# Import data
  df <- readRDS("./data_assamese/df.rds")
  d <- readRDS("./data_assamese/list.rds")
  ID_features <- readRDS("./data_assamese/ID_features.rds")

# dplyr options
  options(dplyr.summarise.inform = FALSE)

1 Empirical distributions

1.1 Histograms

Distribution of observed edges \(y_{[a, b]}\):

c(d$y_ab,
  d$y_ba) %>%
  hist.plot()

Distribution of observed rates (\(y_{[a, b]}/S_{|a, b|}\)):

c(d$y_ab / d$s_ab,
  d$y_ba  / d$s_ab) %>%
  hist.plot(binw = 0.1)

Distribution of sampling effort \(S_{|a, b|}\) (dyad-level):

d$s_ab %>%
  hist.plot() +
  xlim(c(0, 18))

Distribution of sampling effort \(S_{[a]}\) (individual-level):

# y
c(df$S_a, df$S_b) %>%
  unique() %>%
  hist.plot()  +
  ylim(c(0, 15))  +
  xlim(c(0, 10))

1.2 Social network

(Not displayed in the HTML doc)

Show code:

# Max number of observation (to scale width of edges)
  max_lim <- c(d$y_ab, d$y_ba) %>% max()

# Reformatting of data
  d_sn <- list()
  d_sn$id <- ID_features
  d_sn$id$ID <- ID_features$ind
  d_sn$id$x <- ID_features$Ra
  d_sn$id$grp <- d_sn$id$grp 
  d_sn$df <- df
  d_sn$df$grp <- df$gr_n
  d_sn$df$ind_a <- df$ind_a
  d_sn$df$ind_b <- df$ind_b

# SST
  d_sn$id %>% filter(grp == 3)
  
  # Coordinates
  coord_sst <- tibble(
    x = c(4,
          1, 1, 2,
          1, 1, 2, 2, 3, 3),
    y = c(1,
          4, 3, 3,
          2, 1, 2, 1, 2, 1)
  )
  
  # Plot
  sn(data = d_sn, subset_group = TRUE, grp_nb = 3, coord_df = coord_sst,
     col = "continuous", limits = c(1, max_lim), node_size = 9, text_size = 2.5)

  # MST
  d_sn$id %>% filter(grp == 2)
  
  # Coordinates
  coord_mot <- tibble(
    x = c(3, 3,
          4, 4,
          4,
          3,
          1, 1, 1, 2, 2, 2, 2,
          3, 4),
    y = c(3, 2,
          4, 3, 
          2,
          4,
          3, 2, 1, 4, 3, 2, 1,
          1, 1)
  )
  
  # Plot
  sn(data = d_sn, subset_group = TRUE, grp_nb = 1, coord_df = coord_mot,
     col = "continuous", limits = c(1, max_lim), node_size = 9, text_size = 2.5)
  
    # MOT
  d_sn$id %>% filter(grp == 2)
  
  # Coordinates
  coord_mst <- tibble(
    x = c(3, 3, 3, 3, 4, 4, 4, 4,
          5,
          1, 1, 2, 2, 2,
          1, 1, 2,
          5, 5, 5),
    y = c(4, 3, 2, 1, 4, 3, 2, 1,
          1,
          2, 1, 3, 2, 1,
          4, 3, 4,
          4, 3, 2)
  )
  
  # Plot
  sn(data = d_sn, subset_group = TRUE, grp_nb = 2, coord_df = coord_mst,
     col = "continuous", limits = c(1, max_lim), node_size = 9, text_size = 2.5)

2 Prior predictive checks

We start by defining the hyperpriors.

  set.seed(2666)
  n_s <- 1000
  fe <- tibble(  
    sample = c(1:n_s),
    s_G = rexp(n_s, 1),
    s_R = rexp(n_s, 1),
    s_T = rexp(n_s, 1),
    c_GR = rlkjcorr(n_s, 2, eta = 3)[,,1][,2],
    c_TT = rlkjcorr(n_s, 2, eta = 3)[,,1][,2],
    b_Re = rnorm(n_s, 0, 0.6),
    b_Ra_1 = rnorm(n_s, 0, 0.6),
    b_Ra_2 = rnorm(n_s, 0, 0.6),
    D = rnorm(n_s, -1.5, 1)
  )

We then sample individual-level varying effects:

## Individual var effects
  vcov_ind <- list()
  ind_ve <- list()
  for(i in 1:n_s){
    # one var-covar per prior sample: distribution of 1e3 matrices
    vcov_ind[[i]] <- matrix(
      c((fe$s_G[i] * fe$s_G[i]), (fe$c_GR[i] * fe$s_G[i] * fe$s_R[i]),
        (fe$c_GR[i] * fe$s_G[i] * fe$s_R[i]), (fe$s_R[i] * fe$s_R[i])),
      nrow = 2,
      ncol = 2,
      byrow = TRUE
    )
    
    # We draw 20 ind per var covar matrix
    ind_ve[[i]] <- MASS::mvrnorm(45,
                              mu = c(0, 0),
                              Sigma = vcov_ind[[i]]) %>%
      as_tibble() %>%
      rename(., G = V1, R = V2) %>%
      mutate(
        ind = c(1:45),
        sample = i)
  }
  
  # Collapse list to a 45,000 row tibble
  ind_ve <- ind_ve %>% bind_rows() %>%
    mutate(rank = runif(n(), min = 0, max = 1))
  ind_ve %>% head()

# A tibble: 6 × 5
        G       R   ind sample   rank
    <dbl>   <dbl> <int>  <int>  <dbl>
1  0.925  -0.0721     1      1 0.405 
2  1.25   -0.779      2      1 0.821 
3  1.38   -0.994      3      1 0.244 
4 -0.267  -1.01       4      1 0.0355
5 -0.0115  1.03       5      1 0.950 
6 -0.106   0.873      6      1 0.621 

Then, dyad-level varying effects:

## Dyad parameters
  vcov_dyad <- list()
  dyad_ve <- list()
  for(i in 1:n_s){
    # one var-covar per sample
    vcov_dyad[[i]] <- matrix(
      c((fe$s_T[i] * fe$s_T[i]), (fe$c_TT[i] * fe$s_T[i] * fe$s_T[i]),
        (fe$c_TT[i] * fe$s_T[i] * fe$s_T[i]), (fe$s_T[i] * fe$s_T[i])),
      nrow = 2,
      ncol = 2,
      byrow = TRUE
    )
    
    # Sample 340 dyads per var covar matrix
    dyad_ve[[i]] <- MASS::mvrnorm(340,
                                  mu = c(0, 0),
                                  Sigma = vcov_dyad[[i]]) %>%
      as_tibble() %>%
      rename(Tab = V1, Tba = V2) %>%
      mutate(
        dyad = c(1:340),
        sample = i)
  }
  
  # Collapse list to a 340,000 row tibble
  dyad_ve <- dyad_ve %>% bind_rows() %>%
    mutate(rel = sample(c(0, 1), size = n(), replace = TRUE),
           Z = runif(n(), 0, 1))
  dyad_ve %>% head()

# A tibble: 6 × 6
      Tab     Tba  dyad sample   rel     Z
    <dbl>   <dbl> <int>  <int> <dbl> <dbl>
1 -0.0270 -0.357      1      1     1 0.263
2 -0.0107  0.0342     2      1     0 0.698
3 -0.214  -0.366      3      1     1 0.518
4  0.335  -0.435      4      1     1 0.672
5 -0.106  -0.305      5      1     1 0.415
6 -0.173   0.141      6      1     1 0.278

Next, we construct three groups (10, 15, and 20 individuals).

Show code.

## Generate dyads for three groups of respectively 10, 15, 20 individuals
  grp_features <- tibble(
    grp = c(1:3),
    GS = c(10, 15, 20),
    first_ind = lag(GS, default = 0) %>% cumsum() + 1,
    last_ind = first_ind + GS - 1
  )
  
  # individuals 1-10
  dyads <- tibble(
    ind_a = t(combn(grp_features$first_ind[1]:grp_features$last_ind[1], 2))[, 1],
    ind_b = t(combn(grp_features$first_ind[1]:grp_features$last_ind[1], 2))[, 2]
    ) %>%
    # Ind 11-25
    bind_rows(
      tibble(
        ind_a = t(combn(grp_features$first_ind[2]:grp_features$last_ind[2], 2))[, 1],
        ind_b = t(combn(grp_features$first_ind[2]:grp_features$last_ind[2], 2))[, 2]
      )
    ) %>%
    # Ind 26-45
    bind_rows(
      tibble(
        ind_a = t(combn(grp_features$first_ind[3]:grp_features$last_ind[3], 2))[, 1],
        ind_b = t(combn(grp_features$first_ind[3]:grp_features$last_ind[3], 2))[, 2]
      )
    ) %>%
    # dyad number
    mutate(dyad = 1:n()) %>%
    slice(rep(1:n(), each = n_s)) %>%
    mutate(sample = c(1:n_s) %>% rep(length.out = n()))
  # We obtain one row per combination of sample {1:1000} and dyad {1:340}
  nrow(unique(dyads[, c('dyad', 'sample')])) == nrow(dyads) # test

[1] TRUE

We finally generate rates and observations:

## Combine samples and dyads
  prior_sim <- dyads %>%
    left_join(dyad_ve, by = c("sample", "dyad")) %>%
    # Add A attribute
    left_join(ind_ve, by = c("ind_a" = "ind", "sample")) %>%
    rename(Ga = G, Ra = R, Ra_a = rank)  %>%
    # Add B attribute
    left_join(ind_ve, by = c("ind_b" = "ind", "sample")) %>%
    rename(Gb = G, Rb = R, Ra_b = rank) %>%
    # Add population attributes
    left_join(fe %>% select(sample, b_Re, b_Ra_1, b_Ra_2, D), by = "sample") %>%
    
    # Gen quantitites
    mutate(psi_ab = D + Ga + Rb + Tab,
           psi_ba = D + Gb + Ra + Tba,
           m_ab = exp(D + Ga + Rb + Tab +
                      b_Re * rel +
                      ifelse(Ra_a < Ra_b, 
                             b_Ra_1 * (Ra_b - Ra_a),
                             b_Ra_2 * (Ra_b - Ra_a))),
           m_ba = exp(D + Gb + Ra + Tba +
                        b_Re * rel +
                        ifelse(Ra_b < Ra_a, 
                               b_Ra_1 * (Ra_a - Ra_b),
                               b_Ra_2 * (Ra_a - Ra_b))),
           y_ab = rpois(n(), m_ab),
           y_ba = rpois(n(), m_ba))

We plot the rates \(m\):

Show code.

# mab
  prior_sim %>%
    filter(sample < 21) %>%
    select(m_ab, m_ba, sample) %>%
    gather(param, m, 1:2) %>%
    ggplot(aes(x = m, group = sample)) +
    stat_slab(
      slab_color = NA,
      fill = "#d9c2ad",
      scale = 0.9,
      normalize = "groups",
      slab_alpha = 0.2,
      density = "bounded",
      trim = FALSE
    ) +
    
    stat_slab(
      slab_color = "#363533",
      fill = NA,
      slab_linewidth = 0.3,
      scale = 0.9,
      normalize = "groups",
      slab_alpha = 0.3,
      density = "bounded",
      trim = FALSE
    ) +

    theme_bw() +
    theme(
      axis.text.x = element_text(size = 10),
      axis.text.y = element_blank(),
      axis.ticks.y = element_blank(),
      panel.grid = element_blank(),
      panel.grid.major.y = element_line(
        color = "#ccccc0",
        linewidth = 0.3,
        linetype = "dotted"),
      panel.border = element_blank(),
      strip.background = element_rect(fill = "white", color = "white")) +
    labs(y = "", x = "") +
    xlim(c(-1, 24))

Distribution of observations \(y\):

Show code.

 prior_sim %>%
    filter(sample < 21) %>%
    select(y_ab, y_ba, sample) %>%
    gather(param, y, 1:2) %>%
    ggplot(aes(x = y, group = sample)) +
    
    geom_freqpoly(binwidth = 1, 
                  col = "#c4a386",
                  alpha = 0.35,
                  linewidth = 0.5) +
    geom_point(stat = "bin", aes(y = after_stat(count)), 
               binwidth = 1,
               fill = "#c4a386",
               pch = 21,
               colour = "white",
               alpha = 0.7,
               size = 1.7) +
    theme_bw() +
    theme(
      axis.text.x = element_text(size = 10),
      axis.text.y = element_blank(),
      axis.ticks.y = element_blank(),
      panel.grid = element_blank(),
      panel.grid.major.y = element_line(
        color = "#ccccc0",
        linewidth = 0.3,
        linetype = "dotted"),
      panel.border = element_blank(),
      strip.background = element_rect(fill = "white", color = "white")) +
    labs(y = "", x = "") +
    xlim(c(-1, 24))

Observations \(y\) for 10%, 50%, and 90% quantiles of \(m\):

Show code:

  # pred for m_hat
    tibble(m_hat = 
             prior_sim %>% 
             pull(m_ab, m_ba) %>% 
             quantile(c(.1, .5, .9)) %>%
             round(digits = 2)) %>%
    slice(rep(1:n(), each = 1e3)) %>%
    mutate(y = rpois(n(), m_hat)) %>%
      ggplot() +
      geom_histogram(aes(x = y, y = after_stat(ncount)),
                     binwidth = 1,
                     color = "#f7f7f0",
                     linewidth = 0.5,
                     fill = "#d9c2ad") +
      facet_wrap(~ m_hat, ncol = 1) +
      theme_bw() +
      theme(
        axis.text.x = element_text(vjust = 0),
        axis.text.y = element_blank(),
        axis.ticks.y = element_blank(),
        panel.grid = element_blank(),
        panel.grid.major.y = element_line(
          color = "#ccccc0",
          size = 0.3,
          linetype = "dotted"),
        panel.border = element_blank(),
        strip.background = element_rect(fill = "white", color = "white"),
        plot.margin = margin(1, 0, 0, 0, "cm")
      ) +
      labs(y = "", x = "") +
      scale_x_continuous(expand = c(0.02, 0), limits = c(-1, 24))

Distribution of slopes:

Show code:

set.seed(3666)
    prior_sim %>%
      filter(sample %in% sample(1:1000, 24, replace = FALSE)) %>%
      mutate(raw_id = paste0(sample, "_", dyad)) %>%
      expand(nesting(.), X = seq(
        from = 0,
        to = 1,
        length.out = 101
      )) %>%
      mutate(m_ab = exp(psi_ab + b_Re * X),
             m_ba = exp(psi_ba + b_Re * X)) %>%

      # Plot
      ggplot(aes(x = X, y = m_ba, group = raw_id)) +
      # Layout
      theme_bw() +
      facet_wrap(~ sample, ncol = 4) +
      theme(
        axis.text = element_text(size = 8),
        axis.ticks = element_blank(),
        panel.grid.minor = element_blank(),
        panel.grid.major = element_line(
          color = "#c2c2b0",
          size = 0.2,
          linetype = "dotted"
        ), 
        strip.background = element_rect(
          color = "white", fill="white"),
        strip.text = element_blank()
      ) +
      geom_line(alpha = 0.1) +
      ylim(c(-1, 22)) +
      xlim(c(-0.05, 1.05)) +
      labs(x = "", y = "")

3 Posterior model

3.1 Running models

# Stat model 4: Adjusted by relatedness, rank, and sampling effort
srm_1 <- cmdstan_model("./stan_models/04/rel_rank.stan")
m1 <- srm_1$sample(
      data = d,
      iter_warmup = 2e3,
      iter_sampling = 2e3,
      chains = 4,
      parallel_chains = 4
    )  
m1$summary() %>% saveRDS("./fitted_models/05/rel_rank_sum.rds")
m1$draws() %>% saveRDS("./fitted_models/05/rel_rank_draws.rds")
m1 <- m1 %>% tidy_draws() 
m1 %>% saveRDS("./fitted_models/05/rel_rank.rds")

# Stat model 4 as well, with expected values as transformed parameters
srm_2 <- cmdstan_model("./stan_models/04/rel_rank_tp.stan")
m1.2 <- srm_2$sample(
      data = d,
      iter_warmup = 2e3,
      iter_sampling = 2e3,
      chains = 4,
      parallel_chains = 4
    ) %>% tidy_draws()
m1.2 %>% saveRDS("./fitted_models/05/rel_rank_tp.rds")

# Stat model 4': Adjusted by relatedness, rank, sampling effort, and group
srm_3 <- cmdstan_model("./stan_models/04/grp_rel_rank.stan")
m2 <- srm_3$sample(
      data = d,
      iter_warmup = 2e3,
      iter_sampling = 2e3,
      chains = 4,
      parallel_chains = 4
    ) %>% tidy_draws()
m2 %>% saveRDS("./fitted_models/05/grp_rel_rank.rds")

3.2 Marginal posteriors

Import posterior draws and plot them. First, the marginal posterior distribution of the fixed effects:

# Not stratified by group size (stat model 4)
m1 <- readRDS("./fitted_models/05/rel_rank.rds")
m1 %>%
     fp(limo = c(-3.2, 2.5),
     vec_param = c("D", "b_Re", "b_Ra[2]", "b_Ra[1]"))

# Stratified by group size (stat model 4')
m2 <- readRDS("./fitted_models/05/grp_rel_rank.rds")
m2 %>%
  fp(limo = c(-3.2, 2.1),
     vec_param = c("b_Re", "b_Ra[1]", "b_Ra[2]", "d[1]", "d[2]", "d[3]"))

3.3 \(\psi_{[a, b]}\)

\(\psi_{[a, b]}\) is a generated parameter. It is defined as: \[ \psi_{[a, b]} = D + G_{[a]} + R_{[b]} + T_{[a, b]} \]

We show the distribution of \(\psi_{[a, b]}\)’s posterior means:

Show code:

# Extract expected values
m1.2 <- readRDS("./fitted_models/05/rel_rank_tp.rds")

# Posterior means
psi <- m1.2 %>%
  select(starts_with("psi")) %>%
  gather(param, value) %>%
  group_by(param) %>%
  summarise(value = mean(value)) %>%
  pull(value)
  
# 10, 50, and 90% percentiles
psi_hat <- psi %>%
  quantile(c(.1, .5, .9))

# Plot
psi %>% 
  hist.plot(binw = 0.2, fill = "#c4bcaf", linewidth = 0.5) +
  ylim(c(-2, 100)) +
  geom_point(data = tibble(y = 0.2, x = psi_hat), aes(x = x, y = y), 
             col = "white", fill = "#37807e", size = 3, pch = 21)

Scale for y is already present.
Adding another scale for y, which will replace the existing scale.

3.4 Posterior estimates for relatedness

CATE for three baselines \(\psi\).

# Contrasts for the three psi
  a <- (exp(psi_hat[1] + m1$b_Re) -
          exp(psi_hat[1]))
  
  b <- (exp(psi_hat[2]  + m1$b_Re) -
          exp(psi_hat[2]))
  
  c <- (exp(psi_hat[3] + m1$b_Re) -
          exp(psi_hat[3]))

Plot:

Show code:

# Plot
  tibble(theta = c("1", "2", "3") %>% rep(each = 8e3),
         value = c(a, b, c)) %>%
    
    ggplot(aes(
      x = value,
      fill = as.factor(theta),
      group = as.factor(theta)
    )) +
    theme_bw() +
    geom_hline(
      yintercept = 0,
      color = "#b8b5ab",
      linewidth = 0.3,
      linetype = "dotted"
    ) +
    theme(
      legend.position = "none",
      axis.text.y = element_blank(),
      axis.text.x = element_text(vjust = -1.5),
      axis.ticks.y = element_blank(),
      panel.grid = element_blank(),
      panel.grid.major.x = element_line(
        color = "#c2c2b0",
        size = 0.3,
        linetype = "dotted"
      ),
      strip.background = element_rect(fill = "white", color = "white")
    ) + stat_slab(
      slab_color = "#363533",
      slab_linewidth = 0.2,
      scale = 0.7,
      normalize = "groups",
      slab_alpha = 0.5,
      density = "bounded",
      trim = FALSE
    ) +
    labs(x = "", y = "") +
    geom_vline(
      xintercept = 0,
      color = "#6e6d67",
      linewidth = 0.3,
      linetype = "dotted"
    ) +
    scale_fill_manual(values = c("#999388", "#c4bcaf", "#ded6c8")) +
    scale_x_continuous(breaks = (seq(min(-0.4), max(0.4), by = 0.1)) %>%
                         round(1), limits = c(-0.4, 0.4))

Counterfactual outcomes:

# Outcomes for the two values of rel
  a <- exp(m1$D)
  b <- exp(m1$D + m1$b_Re)

Plot:

Show code:

# Plot
  tibble(treatment = c("1", "0") %>% rep(each = 8e3),
         value = c(a, b)) %>%
    ggplot(aes(
      x = value,
      fill = treatment,
      group = treatment,
      linetype = treatment
    )) +
    theme_bw() +
    geom_hline(
      yintercept = 0,
      color = "#b8b5ab",
      linewidth = 0.3,
      linetype = "dotted"
    ) +
    theme(
      legend.position = "none",
      axis.text.y = element_blank(),
      axis.text.x = element_text(vjust = -1.5),
      axis.ticks.y = element_blank(),
      panel.grid = element_blank(),
      panel.grid.major.x = element_line(
        color = "#c2c2b0",
        size = 0.3,
        linetype = "dotted"
      ),
      strip.background = element_rect(fill = "white", color = "white")
    ) +
    
    stat_slab(
      slab_color = "#2b2a2a",
      slab_linewidth = 0.4,
      scale = 0.7,
      normalize = "groups",
      slab_alpha = 0.5,
      density = "bounded",
      trim = FALSE
    ) +
    labs(x = "", y = "") +
    scale_fill_manual(values = c("#c4bcaf", "transparent")) +
    scale_x_continuous(breaks = (seq(min(-0.5), max(0.9), by = 0.1)) %>%
                         round(1), limits = c(0, 0.4))

3.5 Posterior estimates for rank

Rank effect:

# 1e3 samples
  m1_s_mod <- m1 %>% slice(1:1000)

# 9 differences in dominance rank (from -1 to 1)
  d1 <- (1 - 0)
  d2 <- (1 - 0.25)
  d3 <- (1 - 0.5)
  d4 <- (1 - 0.75)
  d5 <- 0
  d6 <- (0 - 0.25)
  d7 <- (0 - 0.5)
  d8 <- (0 - 0.75)
  d9 <- (0 - 1)

# Outcomes for these 9 differences
  s1 <- exp(m1_s_mod$D + m1_s_mod$`b_Ra[1]` * d1)
  s2 <- exp(m1_s_mod$D + m1_s_mod$`b_Ra[1]` * d2)
  s3 <- exp(m1_s_mod$D + m1_s_mod$`b_Ra[1]` * d3)
  s4 <- exp(m1_s_mod$D + m1_s_mod$`b_Ra[1]` * d4)
  s5 <- exp(m1_s_mod$D)
  s6 <- exp(m1_s_mod$D + m1_s_mod$`b_Ra[2]` * d6)
  s7 <- exp(m1_s_mod$D + m1_s_mod$`b_Ra[2]` * d7)
  s8 <- exp(m1_s_mod$D + m1_s_mod$`b_Ra[2]` * d8)
  s9 <- exp(m1_s_mod$D + m1_s_mod$`b_Ra[2]` * d9)

Plot:

Show code:

# Plot
  tibble(
    samples = c(s1, s2, s3, s4, s5, s6, s7, s8, s9),
    X = c(d1, d2, d3, d4, d5, d6, d7, d8, d9) %>% rep(each = 1000)
  ) %>%
    ggplot(aes(x = X, y = samples)) +
    geom_vline(
      xintercept = 0,
      color = "#6e6d67",
      linewidth = 0.4,
      linetype = "dotted"
    ) +
    tidybayes::stat_interval(.width = c(.4, .75, .89), size = 3) +
    scale_color_manual(values = c("#ded6c8", "#c4bcaf", "#999388")) +
    theme_bw() +
    theme(
      legend.position = "none",
      axis.ticks.y = element_blank(),
      panel.grid = element_blank(),
      panel.grid.major = element_line(
        color = "#ccccc0",
        size = 0.4,
        linetype = "dotted"
      ),
      strip.background = element_rect(fill = "white", color = "white")
    ) +
    labs(x = "", y = "") +
    ylim(c(0, 0.22))

Warning: Removed 18 rows containing missing values (`stat_slabinterval()`).

3.6 Posterior predictions

Posterior predictive distribution of \(y_{[a, b]}\).

Show code:

# Extract expected values
set.seed(3666)
m1.2 %>%
  select(starts_with("m_ab")) %>%
  slice(1:40) %>%
  mutate(draw = 1:n()) %>%
  gather(param, value, 1:(ncol(.) - 1)) %>%
  mutate(direction = 1) %>%
  
  bind_rows(m1.2 %>%
  select(starts_with("m_ba")) %>%
  slice(1:40) %>%
  mutate(draw = 1:n()) %>%
  gather(param, value, 1:(ncol(.) - 1)) %>%
  mutate(direction = 2)) %>%
    tibble() %>%
    mutate(m = exp(value),
           y = rpois(n(), m)) %>%
    group_by(draw, y) %>%
    summarise(count = n()) %>%
    
    ggplot(aes(x = y, y = count)) +
    geom_col(data = tibble(y = c(d$y_ab,
  d$y_ba)) %>%
    group_by(y) %>%
    summarise(count = n()),
    color = "#e6e4e1",
    linewidth = 0.1,
    fill = "#27495c") +
    
    geom_line(aes(group = draw),
              col = "#9e6a7d",
              alpha = 0.3,
              linewidth = 0.3) + 
    geom_point(aes(group = draw),
               fill = "#9e6a7d",
               pch = 21,
               colour = "white",
               size = 2,
               alpha = 0.6) +

    theme_bw() +
    theme(
    axis.text.x = element_text(size = 10),
    axis.ticks.y = element_blank(),
    panel.grid = element_blank(),
    panel.grid.major.y = element_line(
      color = "#ccccc0",
      linewidth = 0.3,
      linetype = "dotted"),
    panel.border = element_blank(),
    strip.background = element_rect(fill = "white", color = "white"),
    plot.margin = margin(1, 0, 0, 0, "cm")) +
  labs(y = "", x = "")

Dyad-specific posterior predictive distribution of \(y_{[a, b]}\).

Show code:

emp_data <- df %>% 
  select(dyad, y_ab, y_ba) %>%
  mutate(dyad = paste0("m[", dyad, "]")) %>%
  slice(1:9) %>%
  rename("1" = y_ab, "2" = y_ba, param = dyad) %>%
  gather(direction, y, 2:3) %>%
  mutate(direction = as.numeric(direction))

m1.2 %>%
  select(starts_with("m_ab")) %>%
  select(1:9) %>%
  gather(param, value, 1:9) %>%
  mutate(across("param", \(x) str_replace(x, 'm_ab', 'm'))) %>%
  
  mutate(direction = 1) %>% bind_rows(
    
  m1.2 %>%
  select(starts_with("m_ba")) %>%
  select(1:9) %>%
  gather(param, value, 1:9)  %>%
  mutate(across("param", \(x) str_replace(x, 'm_ba', 'm'))) %>%
  mutate(direction = 2)
  ) %>%
  mutate(m = exp(value),
         y = rpois(n(), m)) %>%
  
  ggplot(aes(x = y)) +
  geom_histogram(binwidth = 1,
               fill = "#e0ccd3",
               colour = "white") +
  facet_grid(param ~ direction) +
    theme_bw() +
    theme(
    axis.text.y = element_blank(),
    axis.text.x = element_text(size = 10),
    axis.ticks.y = element_blank(),
    panel.grid = element_blank(),
    panel.grid.major.y = element_blank(),
    panel.border = element_blank(),
    strip.background = element_rect(fill = "white", color = "white"),
    plot.margin = margin(0, 0, 0, 0, "cm")
    ) +
    geom_hline(yintercept = 0, color = "#6e6d67", linewidth = 0.3, linetype = "dotted") +
  labs(y = "", x = "") +
  
  geom_point(data = emp_data,
             aes(y = 0),
             pch = 21,
             fill = "#27495c",
             color = "white",
             size = 2
             )

4 MCMC diagnostics

4.1 Rhat

Show code:

# Rhats
  m1_sum <- readRDS("./fitted_models/05/rel_rank_sum.rds")
  m1_sum[, 8] %>%
    pull(rhat) %>%
    hist.plot(binw = 0.0001) +
    ylim(c(-1, 90))

Show code:

# ESS bulk
  m1_sum[, 9] %>%
    pull(ess_bulk) %>%
    hist.plot(binw = 500) +
     geom_vline(xintercept = 500, linewidth = 0.4, linetype = "dotted",
                color = "#ccccc0") +
    ylim(c(-1, 80)) +
    xlim(c(-1, 20500))

Show code:

# ESS tail
  m1_sum[, 10] %>%
    pull(ess_tail) %>%
    hist.plot(binw = 150) +
     geom_vline(xintercept = 500, linewidth = 0.4, linetype = "dotted",
                color = "#ccccc0") +
    ylim(c(-1, 130))

Traceplots:

Show code:

# Traceplot
  readRDS("./fitted_models/05/rel_rank_draws.rds") %>%
    bayesplot::mcmc_trace(
      regex_pars = c("b_Re", "D", "b_Ra", "s_G",
                     "s_R", "s_T", "c_GR",
                     "c_TT"),
      size = 0.1
    ) +
    scale_color_manual(values = c('#F6D99D', "#D58761", '#77A4B9', '#225477')) +
    theme_bw() +
    theme(
      axis.text.x = element_text(size = 10),
      axis.ticks.y = element_blank(),
      panel.grid = element_blank(),
      panel.grid.major.y = element_line(
        color = "#ccccc0",
        linewidth = 0.3,
        linetype = "dotted"
      ),
      panel.border = element_rect(linewidth = 0.4),
      legend.position = "none",
      strip.background = element_rect(fill = "white", color = "white"),
      plot.margin = margin(1, 1, 1, 1, "cm")
    )